OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Molecular Evolution is 2. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-05-01 to 2026-05-01.)

Article	Citations
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	43
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	42
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	39
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	29
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	29
Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing	26
Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin	24
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	22
The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny	21
How Binding Affinity and Binding Specificity Map to Sequence Space	19
Screening for Viruses in Pallas’s Long-Tongued Bats (Glossophaga soricina) in Brazil	17
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	17
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	16
Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity	15
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	15
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	15
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	15
Understanding Functional Evolution in Orthologs and Paralogs	14
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	14
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	14
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	14
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	13
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	12
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	12
MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems	12

On Protein Loops, Prior Molecular States and Common Ancestors of Life	11
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	11
Mapping Patterns of G-Quadruplex-Forming Sequence Conservation in Primates	11
dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	11
Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes	11
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	10
Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model	10
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	10
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	10
2025 Zuckerkandl Prize	10
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	10
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	10
Cystathionine Gamma-Lyase: A Potential Longevity Gene Under Selection?	10
Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	9
Type II LDH/MDH Oxidoreductases in Pacific Oyster Magallana gigas (Thunberg, 1793): Gene Organization and Expression Patterns During Development and Across Tissues	9
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	9
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	9
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	8
Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins	8
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	8
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	8
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	8
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	7
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	7
Informatic Capabilities of Translation and Its Implications for the Origins of Life	7
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Therm	7
A New View of the Last Universal Common Ancestor	7
Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity	7
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	6
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees	6
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	6
Decoding the Evolution and Co-Phospho-Regulatory Networks of SHROOM Proteins	6
Correlated Evolution Drives Structural Convergence of Interacting Proteins	6
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	6
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	6
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	6
Origins and Functional Significance of Eukaryotic Protein Folds	6
Caspase Domain Duplication During the Evolution of Caspase-16	6
Genetic Exchanges Shape the Evolutionary Diversification Among Shigella phages	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences	5
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	5

Main Factors Shaping Amino Acid Usage Across Evolution	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	4
2022 Zuckerkandl Prize	4
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	4
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration	4
How Many Factors Influence Genomic GC Content Among Prokaryotes?	4
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	4
The GFI1 Gene Family: Evolution, Structure, and Its Role in Immune Responses	4
A Genomic Conceptualization of Species	4
2024 Zuckerkandl Prize	4
Replication Rate-Information Storage Trade-Off Shapes Genome Architecture Across Domains	4
APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families	4
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	4
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	4
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	4
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
Decay of Skin-Specific Gene Modules in Pangolins	3
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
On the Unknown Proteins of Eukaryotic Proteomes	3
A Bayesian Framework for the Network Analysis of Transmission Dynamics in Infectious Disease	3
First Report on Presence of Mitochondrial Introns in Freshwater Sponges, and Pseudogenic Evidence of Their Loss	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3	3
Efficiency of Ancestral Inference and Characterization of Genetic Structure of Chinese Kazakh Group with a Novel InDel Panel	3
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data	3
NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes	3
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	3
Evolution of the Major Components of Innate Immunity in Animals	3
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	3
A Multi-level Perspective on the Evolution of Orthologs and Their Functions	3
Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds	2
Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails	2
Fascination with RNA Editing: In the Lights of Evolution and Biology	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution	2
Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species	2
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	2
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events	2
Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks	2
Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition	2
nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models	2
Clay Minerals, Panacea or Parameter in RNA Oligomerization?	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
Human Riboviruses: A Comprehensive Study	2
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	2
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
Functional Diversification and the Plant Secondary Cell Wall	2
Expansion and Diversification of the 14-3-3 Gene Family in Camellia sinensis	2
In Silico Investigation of the Interactions Between Cotton Leaf Curl Multan Virus Proteins and the Transcriptional Gene Silencing Factors of Gossypium hirsutum L.	2
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	2
Lectin Gene Families in Three Phaseolus Species: Genome-Wide Identification, Evolutionary Analysis, Pleiotropic Effect, and Regulation Under Multiple Stress Conditions	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	2
The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	2
Best Practices in Microbial Experimental Evolution	2
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Functional Divergence and Origin of the Vertebrate Praja Family	2